Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.
In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.
Chain identifier: A
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: What type of B-factor?
WHAT IF does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. TLS seems not mentioned in the header of the PDB
file. But anyway, if WHAT IF complains about your B-factors, and you think
that they are OK, then check for TLS related B-factor problems first.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :298.000
Warning: More than 2 percent of buried atoms has low B-factor
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 2.27
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
110 TYR ( 114-) A
62 PHE ( 66-) A 221 PHE ( 226-) A
37 ASP ( 41-) A 67 ASP ( 71-) A 160 ASP ( 165-) A 170 ASP ( 175-) A
182 GLU ( 187-) A 233 GLU ( 238-) A
13 HIS ( 17-) A CG ND1 CE1 109.61 4.0 92 HIS ( 96-) A N CA C 99.82 -4.1 203 THR ( 208-) A N CA C 99.12 -4.3
37 ASP ( 41-) A 67 ASP ( 71-) A 160 ASP ( 165-) A 170 ASP ( 175-) A 182 GLU ( 187-) A 233 GLU ( 238-) A
202 VAL ( 207-) A 5.74 203 THR ( 208-) A 4.36 92 HIS ( 96-) A 4.23 193 LEU ( 198-) A 4.19 62 PHE ( 66-) A 4.15
Tau angle RMS Z-score : 1.568
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.
171 PHE ( 176-) A -2.4 56 LEU ( 60-) A -2.4 79 PRO ( 83-) A -2.3 158 VAL ( 163-) A -2.2 152 LEU ( 157-) A -2.2 162 ILE ( 167-) A -2.2 46 SER ( 50-) A -2.1 51 THR ( 55-) A -2.1 88 GLN ( 92-) A -2.0
Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.
25 SER ( 29-) A PRO omega poor 60 HIS ( 64-) A Poor phi/psi 107 LYS ( 111-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 196 PRO ( 201-) A PRO omega poor 198 LEU ( 203-) A Poor phi/psi 238 ASP ( 243-) A Poor phi/psi 247 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.681
For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.
A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!
3 TYR ( 7-) A 0 6 HIS ( 10-) A 0 11 HIS ( 15-) A 0 12 TRP ( 16-) A 0 15 ASP ( 19-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 46 SER ( 50-) A 0 49 GLN ( 53-) A 0 50 ALA ( 54-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 71 ASP ( 75-) A 0 72 LYS ( 76-) A 0 73 ALA ( 77-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0 81 ASP ( 85-) A 0 88 GLN ( 92-) A 0 99 GLN ( 103-) A 0And so on for a total of 116 lines.
Standard deviation of omega values : 2.183
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
124 GLY ( 129-) A 1.51 12
196 PRO ( 201-) A 0.45 HIGH 232 PRO ( 237-) A 0.45 HIGH
150 PRO ( 155-) A -119.9 half-chair C-delta/C-gamma (-126 degrees)
The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.
The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
46 SER ( 50-) A OG <-> 76 LYS ( 80-) A NZ 0.16 2.54 INTRA 36 TYR ( 40-) A CE2 <-> 256 LYS ( 261-) A NZ 0.16 2.94 INTRA 91 MET ( 95-) A SD <-> 93 VAL ( 97-) A CG2 0.15 3.25 INTRA 68 ASP ( 72-) A OD2 <-> 119 TRP ( 123-) A NE1 0.14 2.56 INTRA BL 11 HIS ( 15-) A ND1 <-> 14 LYS ( 18-) A NZ 0.14 2.86 INTRA BL 36 TYR ( 40-) A CZ <-> 256 LYS ( 261-) A NZ 0.12 2.98 INTRA 103 HIS ( 107-) A NE2 <-> 189 TYR ( 194-) A OH 0.10 2.60 INTRA BL 5 LYS ( 9-) A NZ <-> 10 GLU ( 14-) A OE2 0.08 2.62 INTRA BF 4 GLY ( 8-) A O <-> 8 GLY ( 12-) A N 0.07 2.63 INTRA 99 GLN ( 103-) A NE2 <-> 238 ASP ( 243-) A OD1 0.05 2.65 INTRA BL 26 PRO ( 30-) A O <-> 244 GLN ( 249-) A N 0.05 2.65 INTRA BL 71 ASP ( 75-) A OD1 <-> 85 ARG ( 89-) A NE 0.04 2.66 INTRA 131 GLN ( 136-) A N <-> 132 GLN ( 137-) A N 0.04 2.56 INTRA BL 28 ASP ( 32-) A OD1 <-> 107 LYS ( 111-) A N 0.03 2.67 INTRA BL 47 TYR ( 51-) A OH <-> 118 HIS ( 122-) A NE2 0.03 2.67 INTRA BL 97 ASP ( 101-) A OD1 <-> 222 ARG ( 227-) A NH2 0.01 2.69 INTRA BL
Chain identifier: A
Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.
6 HIS ( 10-) A -5.83 96 LEU ( 100-) A -5.04
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: HIS, ASN, GLN side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
173 ASN ( 178-) A
Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.
Waters are not listed by this option.
27 VAL ( 31-) A N 41 LYS ( 45-) A N 49 GLN ( 53-) A N 70 GLN ( 74-) A N 72 LYS ( 76-) A NZ 91 MET ( 95-) A N 96 LEU ( 100-) A N 120 ASN ( 124-) A ND2 195 THR ( 200-) A N 199 LEU ( 204-) A N 224 LEU ( 229-) A N 225 ASN ( 230-) A ND2 228 GLY ( 233-) A N 255 PHE ( 260-) A N Only metal coordination for 92 HIS ( 96-) A NE2
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
259 HOH ( 324 ) A O 1.06 K 5
28 ASP ( 32-) A H-bonding suggests Asn 234 GLU ( 239-) A H-bonding suggests Gln
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.107 2nd generation packing quality : 0.505 Ramachandran plot appearance : -1.554 chi-1/chi-2 rotamer normality : -1.681 Backbone conformation : -0.832
Bond lengths : 0.573 (tight) Bond angles : 0.817 Omega angle restraints : 0.397 (tight) Side chain planarity : 0.628 (tight) Improper dihedral distribution : 1.110 B-factor distribution : 0.860 Inside/Outside distribution : 0.956
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.
Resolution found in PDB file : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : 0.3 Ramachandran plot appearance : -0.9 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : -1.0
Bond lengths : 0.573 (tight) Bond angles : 0.817 Omega angle restraints : 0.397 (tight) Side chain planarity : 0.628 (tight) Improper dihedral distribution : 1.110 B-factor distribution : 0.860 Inside/Outside distribution : 0.956 ==============
WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform Bond lengths and angles, protein residues R.Engh and R.Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392--400 (1991). Bond lengths and angles, DNA/RNA G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman, New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D52, 57--64 (1996). DSSP W.Kabsch and C.Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features Biopolymers 22, 2577--2637 (1983). Hydrogen bond networks R.W.W.Hooft, C.Sander and G.Vriend, Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures PROTEINS, 26, 363--376 (1996). Matthews' Coefficient B.W.Matthews Solvent content of Protein Crystals J. Mol. Biol. 33, 491--497 (1968). Protein side chain planarity R.W.W. Hooft, C. Sander and G. Vriend, Verification of protein structures: side-chain planarity J. Appl. Cryst. 29, 714--716 (1996). Puckering parameters D.Cremer and J.A.Pople, A general definition of ring puckering coordinates J. Am. Chem. Soc. 97, 1354--1358 (1975). Quality Control G.Vriend and C.Sander, Quality control of protein models: directional atomic contact analysis, J. Appl. Cryst. 26, 47--60 (1993). Ramachandran plot G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations J. Mol. Biol. 7, 95--99 (1963). Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994). Ion Checks I.D.Brown and K.K.Wu, Empirical Parameters for Calculating Cation-Oxygen Bond Valences Acta Cryst. B32, 1957--1959 (1975). M.Nayal and E.Di Cera, Valence Screening of Water in Protein Crystals Reveals Potential Na+ Binding Sites J.Mol.Biol. 256 228--234 (1996). P.Mueller, S.Koepke and G.M.Sheldrick, Is the bond-valence method able to identify metal atoms in protein structures? Acta Cryst. D 59 32--37 (2003). Checking checks K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. Who checks the checkers J.Mol.Biol. (1998) 276,417-436.